Variant report

Variant	rs1042338
Chromosome Location	chr6:30152789-30152790
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30146840..30149453-chr6:30151238..30153459,2	K562	blood:

Extended variants
information (count: 125 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs1076229	0.83[EUR][1000 genomes]
rs13194768	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1419671	0.83[EUR][1000 genomes]
rs1419672	0.86[EUR][1000 genomes]
rs1419673	0.83[EUR][1000 genomes]
rs1541324	0.85[EUR][1000 genomes]
rs1573297	0.83[EUR][1000 genomes]
rs1573298	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1573299	0.83[EUR][1000 genomes]
rs17194607	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2239530	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2285795	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2285796	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2508030	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2508031	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2517606	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2517616	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2517653	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2517655	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2844775	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2857433	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2857435	0.85[EUR][1000 genomes]
rs2857438	0.84[EUR][1000 genomes]
rs2857439	0.85[EUR][1000 genomes]
rs2857440	0.84[EUR][1000 genomes]
rs3778622	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3815079	0.80[EUR][1000 genomes]
rs3815080	0.85[EUR][1000 genomes]
rs3815082	0.85[EUR][1000 genomes]
rs3815084	0.85[EUR][1000 genomes]
rs3815085	0.85[EUR][1000 genomes]
rs3815086	0.85[EUR][1000 genomes]
rs3888580	0.83[EUR][1000 genomes]
rs4392759	0.84[EUR][1000 genomes]
rs4711211	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4713293	0.83[EUR][1000 genomes]
rs4959011	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4959012	0.84[EUR][1000 genomes]
rs4959044	0.83[EUR][1000 genomes]
rs757259	0.83[EUR][1000 genomes]
rs757261	0.84[EUR][1000 genomes]
rs757262	0.83[EUR][1000 genomes]
rs757263	0.86[EUR][1000 genomes]
rs757264	0.86[EUR][1000 genomes]
rs7843	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261433	0.81[EUR][1000 genomes]
rs9261440	0.87[EUR][1000 genomes]
rs9261442	0.83[EUR][1000 genomes]
rs9261443	0.87[EUR][1000 genomes]
rs9261444	0.83[EUR][1000 genomes]
rs9261445	0.83[EUR][1000 genomes]
rs9261446	0.83[EUR][1000 genomes]
rs9261448	0.84[EUR][1000 genomes]
rs9261449	0.81[EUR][1000 genomes]
rs9261450	0.87[EUR][1000 genomes]
rs9261451	0.87[EUR][1000 genomes]
rs9261453	0.87[EUR][1000 genomes]
rs9261454	0.83[EUR][1000 genomes]
rs9261455	0.87[EUR][1000 genomes]
rs9261456	0.83[EUR][1000 genomes]
rs9261457	0.83[EUR][1000 genomes]
rs9261458	0.83[EUR][1000 genomes]
rs9261459	0.82[EUR][1000 genomes]
rs9261461	0.85[EUR][1000 genomes]
rs9261462	0.83[EUR][1000 genomes]
rs9261463	0.83[EUR][1000 genomes]
rs9261465	0.83[EUR][1000 genomes]
rs9261466	0.83[EUR][1000 genomes]
rs9261467	0.83[EUR][1000 genomes]
rs9261468	0.83[EUR][1000 genomes]
rs9261470	0.83[EUR][1000 genomes]
rs9261471	0.85[EUR][1000 genomes]
rs9261472	0.84[EUR][1000 genomes]
rs9261473	0.85[EUR][1000 genomes]
rs9261479	0.85[EUR][1000 genomes]
rs9261480	0.84[EUR][1000 genomes]
rs9261482	0.84[EUR][1000 genomes]
rs9261483	0.86[EUR][1000 genomes]
rs9261484	0.83[EUR][1000 genomes]
rs9261485	0.84[EUR][1000 genomes]
rs9261486	0.84[EUR][1000 genomes]
rs9261488	0.85[EUR][1000 genomes]
rs9261489	0.85[EUR][1000 genomes]
rs9261490	0.86[EUR][1000 genomes]
rs9261491	0.86[EUR][1000 genomes]
rs9261492	0.86[EUR][1000 genomes]
rs9261493	0.81[EUR][1000 genomes]
rs9261495	0.85[EUR][1000 genomes]
rs9261496	0.86[EUR][1000 genomes]
rs9261497	0.86[EUR][1000 genomes]
rs9261498	0.85[EUR][1000 genomes]
rs9261499	0.83[EUR][1000 genomes]
rs9261500	0.84[EUR][1000 genomes]
rs9261501	0.84[EUR][1000 genomes]
rs9261502	0.85[EUR][1000 genomes]
rs9261503	0.82[EUR][1000 genomes]
rs9261504	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9261505	0.83[EUR][1000 genomes]
rs9261507	0.85[EUR][1000 genomes]
rs9261508	0.85[EUR][1000 genomes]
rs9261509	0.85[EUR][1000 genomes]
rs9261511	0.85[EUR][1000 genomes]
rs9261513	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9261514	0.83[EUR][1000 genomes]
rs9261517	0.85[EUR][1000 genomes]
rs9261518	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9261519	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9261521	0.83[EUR][1000 genomes]
rs9261522	0.83[EUR][1000 genomes]
rs9261523	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9261524	0.85[EUR][1000 genomes]
rs9261525	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9261526	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9261527	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261528	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9261529	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9261530	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9261531	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9261532	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9261533	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9261535	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs929156	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9357094	0.87[ASN][1000 genomes]
rs9380159	0.88[ASN][1000 genomes]
rs957765	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1042338	HLA-H	cis	multi-tissue	Pritchard
rs1042338	HIST1H2AM	cis	parietal	SCAN
rs1042338	HLA-A	Cis_1M	lymphoblastoid	RTeQTL
rs1042338	BTN2A1	cis	cerebellum	SCAN
rs1042338	NDUFS1	trans	multi-tissue	Pritchard
rs1042338	KIT	trans	multi-tissue	Pritchard
rs1042338	HCG4	cis	multi-tissue	Pritchard
rs1042338	ZKSCAN3	cis	cerebellum	SCAN
rs1042338	TFG	trans	multi-tissue	Pritchard
rs1042338	HLA-G	cis	multi-tissue	Pritchard
rs1042338	HIST1H2BN	cis	parietal	SCAN
rs1042338	HIST1H2AI	cis	parietal	SCAN
rs1042338	HLA-A	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30145000-30173800	Weak transcription	Right Atrium	heart
2	chr6:30148000-30155000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr6:30148000-30173000	Weak transcription	Fetal Heart	heart
4	chr6:30148200-30154800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:30148400-30154000	Weak transcription	HUVEC	blood vessel
6	chr6:30149000-30152800	Weak transcription	Fetal Brain Male	brain
7	chr6:30149000-30156400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:30149200-30157400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:30149400-30152800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:30149400-30153200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:30149400-30153400	Weak transcription	A549	lung
12	chr6:30149600-30153000	Weak transcription	Osteobl	bone
13	chr6:30149600-30155000	Weak transcription	NHEK	skin
14	chr6:30149800-30153400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:30149800-30153400	Weak transcription	Pancreas	Pancrea
16	chr6:30150000-30152800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:30150000-30153000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:30150000-30155000	Weak transcription	HSMM	muscle
19	chr6:30150000-30156400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:30150200-30153000	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:30150200-30156400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:30150200-30163400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:30150400-30152800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr6:30150400-30152800	Weak transcription	Small Intestine	intestine
25	chr6:30150400-30154800	Weak transcription	Fetal Lung	lung
26	chr6:30150400-30157000	Weak transcription	Fetal Kidney	kidney
27	chr6:30150600-30153200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr6:30150600-30153400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:30150600-30179200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr6:30150800-30152800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:30150800-30153200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:30150800-30153200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:30150800-30156200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:30151000-30152800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:30151000-30153400	Weak transcription	Stomach Mucosa	stomach
36	chr6:30151000-30154000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:30151000-30154200	Weak transcription	NH-A	brain
38	chr6:30151200-30153200	Weak transcription	Colonic Mucosa	Colon
39	chr6:30151200-30153400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:30151600-30161400	Strong transcription	Primary T cells from cord blood	blood
41	chr6:30151800-30155000	Strong transcription	Brain Substantia Nigra	brain
42	chr6:30151800-30158200	Strong transcription	Brain Cingulate Gyrus	brain
43	chr6:30151800-30160400	Strong transcription	Thymus	Thymus
44	chr6:30151800-30160600	Strong transcription	Fetal Intestine Small	intestine
45	chr6:30151800-30170400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr6:30152000-30152800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:30152000-30153000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr6:30152000-30153400	Strong transcription	Brain Angular Gyrus	brain
49	chr6:30152000-30157200	Strong transcription	Primary hematopoietic stem cells	blood
50	chr6:30152000-30159200	Strong transcription	Brain Anterior Caudate	brain

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